"get_area" - Surface Areas of Atoms

This section provides a tutorial on how to use the 'get_area' command to measure surface areas of atoms.

PyMol allows you to measure surface areas of the atoms, using the "get_area" command.

For example, the following commands print areas of the carbon atom a hydrogen atom of the methane molecule:

PyMOL># load the carbon atom
PyMOL>load Carbon-Atom.sdf

PyMOL># add 4 hydrogen atoms to create methane
PyMOL>h_add

PyMOL># print surface area of the carbon atom
PyMOL>get_area id 1
 cmd.get_area: 15.171 Angstroms^2.

PyMOL># print surface area of a hydrogen atom
PyMOL>get_area id 2
 cmd.get_area: 8.258 Angstroms^2.

Based the above output, we can calculate the radius of each atom, using the sphere surface area formula: area = 4 * PI * radius * radius.

PyMOL>import math

PyMOL>print str( math.sqrt(15.171/(4*3.14159)) )
1.098758772689268

PyMOL>print str( math.sqrt(8.258/(4*3.14159)) )
0.8106487001768432

Now we can calculate the distance between these 2 atoms. Then we can compare the distance with their radiuses and see how much they overlap with each other:

PyMOL>get_distance id 1, id 2
 cmd.get_distance: 1.090 Angstroms.

If our calculation is correct, half of the hydrogen atom is overlapped with the carbon atom. This can be verified by displaying atoms as spheres.

PyMOL>show spheres, id 1

PyMOL>show spheres, id 2
Surface Areas of Atoms in PyMol
Surface Areas of Atoms in PyMol

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

 RDKit: Open-Source Cheminformatics Software

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

PyMol Measurement Functions

 "get_extent" - Picked Atom Location

 "label" - Generate Labels on Atoms

 Distance between Atoms in PyMol

 Angle Formed by 3 Atoms in PyMol

 Dihedral Angle Formed by 3 Atoms in PyMol

 Use Selection Expressions in PyMol

"get_area" - Surface Areas of Atoms

 Surface Area of Bonded Atoms

 Surface Area of Entire Molecule

 "get_position" - Viewing Center

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB